estLibSize: estimate the library size

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

estimate the library size

Description

estimate the library size of bam files

Usage

estLibSize(bamfiles, index = bamfiles, ...)

Arguments

bamfiles	The file names of the 'BAM' ('SAM' for asBam) files to be processed.
index	The names of the index file of the 'BAM' file being processed; this is given without the '.bai' extension.
...	Not used.

Value

numberic vector

Author(s)

Jianhong Ou

Examples

    if(interactive() || Sys.getenv("USER")=="jianhongou"){
        path <- system.file("extdata", "reads", package="MMDiffBamSubset")
        if(file.exists(path)){
            WT.AB2 <- file.path(path, "WT_2.bam")
            Null.AB2 <- file.path(path, "Null_2.bam")
            Resc.AB2 <- file.path(path, "Resc_2.bam")
            estLibSize(c(WT.AB2, Null.AB2, Resc.AB2))
        }
    }

jianhong/ChIPpeakAnno documentation built on Feb. 2, 2024, 3:26 p.m.